利用monoids整合基因组和代谢参数,预测调节级联中的表型。

IF 1.9 4区 生物学 Q2 BIOLOGY
Marco Polo Castillo-Villalba , Yair Romero , Pedro Miramontes
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引用次数: 0

摘要

分子网络建模需要使用数学和计算形式来进行稳健和准确的表型预测。此外,有必要将这些形式扩展到大规模分子网络,从而有助于理解生物复杂性。在这项工作中,我们提出了一个建模框架的扩展,称为设计原则,由M.A. Savageau开发,基于幂律建模。虽然幂律模型已被证明对理解分子网络的各种特性有价值,但它不允许推断动力学顺序,而动力学顺序通常与分子中存在的结合位点的数量有关。我们通过修改传统的方法来结合monoids的使用来解决这一限制,从而引入了一种新的方法框架,我们称之为基因型算法。由此产生的组合对象定义了一组几何点,这些点在指数空间中的固定点施加了一组约束,这些约束决定了在幂律模型中使用的适当的动力学顺序。这一特性可以预测调控序列中的结合强度和/或DNA结合位点的数量,以及酶动力学中的反应顺序。为了证明本方法的适用性,我们说明了如何在由3到9个反应形成的代谢途径中,在终产物抑制与中间催化反应和单基因抑制的变构系统中,结合位点的数量可以近似。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Using monoids for the integration of genomic and metabolic parameters in the prediction of phenotypes in regulatory cascades
Molecular network modeling requires the use of mathematical and computational formalisms for a robust and accurate prediction of phenotypes. Furthermore, there is a need to extend these formalisms to be applied to large-scale molecular networks, thus helping in the understanding of biological complexity. In this work, we propose an extension of the modeling framework known as design principles, developed by M.A. Savageau, which is based on power-law modeling. While power-law modeling has proven valuable for understanding various properties of molecular networks, it does not allow for the inference of kinetic orders, which are typically associated with the number of binding sites present in molecules. We address this limitation by modifying the traditional approach to incorporate the use of monoids, thereby introducing a novel methodological framework we call Genotype Arithmetic. The resulting combinatorial object defines a family of geometric points, whose fixed points in the exponent space impose a set of constraints that determine the appropriate kinetic order to be used in the power law models. This feature enables a prediction of the binding strength and/or the number of DNA binding sites in regulatory sequences, as well as the reaction orders in enzymatic kinetics. To demonstrate the applicability of the present approach, we illustrated how the number of binding sites can be approximated in metabolic pathways formed by 3 to 9 reactions, in allosteric systems of end-product inhibition with intermediate catalytic reactions and one gene inhibition.
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来源期刊
Biosystems
Biosystems 生物-生物学
CiteScore
3.70
自引率
18.80%
发文量
129
审稿时长
34 days
期刊介绍: BioSystems encourages experimental, computational, and theoretical articles that link biology, evolutionary thinking, and the information processing sciences. The link areas form a circle that encompasses the fundamental nature of biological information processing, computational modeling of complex biological systems, evolutionary models of computation, the application of biological principles to the design of novel computing systems, and the use of biomolecular materials to synthesize artificial systems that capture essential principles of natural biological information processing.
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